Xenbase Release 3.11.0
Highlights of Xenbase v3.11.0
- Transgene links added to gene pages (example: http://test.xenbase.org/gene/showgene.do?method=display&geneId=482739& )
- RRID field added for antibodies
- Proper name display for lines, transgenes, and strains (italic + superscript part)
- Reformatted the "Cite Xenbase" page; added Xenbase publications
Highlights of Xenbase v3.10.0
- The options for gene search (http://test.xenbase.org/gene/gene.do) now actually work. Previously only symbol and synonym search were working, most probably for performance reasons on the old hardware.
- In the upper right-hand minibar it is now possible to search for text containing “+”
- Users can now search for ORFeomes, lines, strains, and transgenes using their Xenbase accession IDs
- It wasn’t possible to edit transgene attributions. Fixed.
- It wasn’t possible to curate images using oocyte development stages. Fixed.
- Time-course X. tropicalis expression data from Owens, Blitz et al. (2016) now available on gene page Expression tab.
- In a related change, many of the expression links from the Summary tab have been moved to the Expression tab.
Highlights of Xenbase v3.8
- Added IMPC mouse phenotype gene page links
- Added PANTHER GO search links on gene pages
- Added XenMine links on gene pages (Data Mining section)
- Reformatted stock centre search and display
- Bug fixes and enhancements
- Added fruit fly and worm ortholog links on gene pages
- Added XenMine links on the landing page
- Added GeneCards to the list of human MODs
- Added MalaCards, OMIM, DECIPHER, and KEGG Disease phenotype search links on gene pages
- Added Ensembl, Protein Atlas, Allen Brain Atlas, and Eurexpress links to the new ortholog "Gene Expression" column on gene pages
- Added Ensembl tropicalis link to gene pages' "expression" section
- Replaced gene page phenotype links for ZFIN (broken) and MGI with symbol search links
- Bug fixes and enhancements
Revised "Genomes" and "Download & Submit Data" menus
More updates FTP landing page for data downloads
Added new genomes - Xenopus laevis 9.1, Xenpus laevis mitochondrial, Xenopus tropicalis 9.0
Xenopus laevis genome v8.0 has been retired due to missing regions - it will still be available for those who have referenced it in the past
Updated ORFeome v1.0 search and search results
Morpholinos on Xenbase!! Morpholino antisense oligos (MOs) are widely used in Xenopus to suppress gene function. Xenbase has introduced a comprehensive catalog of ~1585 published MOs so researchers can quickly identify effective Xenopus specific reagents.
laevis-only genes now display on gene pages
Latest XAO update added
Genome Builds & Gene Models:
Outbred X. laevis genome
X. laevis v7.2 annotation/gene model is now shown on the v7.1 genome build on GBrowse
X. laevis L and S (long and short) genomes now on GBrowse
We are working on reconciling X. laevis L & S alleles on gene pages
X. tropicalis genome build v8.0 has more gene names assigned on GBrowse
GBrowse snapshots are bigger and crisper on gene pages
Human Disease Associations:
Single-gene disease associations are now on ~14,600 gene pages, facilitating direct comparison of information from Xenopus genes with their human orthologs (e.g. tgfb1). Diseases can be searched using OMIM ID from the main search menu.
Transgenes Naming Guidelines:
Xenbase is drafting an updated ‘Xenopus Transgenic Nomenclature Guidelines’ in consultation with the NXR, EXRC and NBRP, and gene nomenclature committee. These guidelines are based on the well-established rules for zebrafish and mouse, with the goal of increasing experimental reproducibility and data clarity cross model organisms. Authors are strongly encouraged to follow the guidelines when naming transgenes or mutant or transgenic Xenopus lines. Contact Xenbase (firstname.lastname@example.org) with comments/questions and for help naming your constructs.
A discussion forum/community bulletin board to discuss and ask advice on all aspects of Xenopus research (e.g., experimental design & data analysis for ChipSeq, RNASeq, Morpholinos, ISH, genes etc.).
More details of the recent updates to Xenbase are detailed in:
Xenbase: Core features, data acquisition, and data processing.
James-Zorn C, Ponferrada VG, Burns KA, Fortriede JD, Lotay VS, Liu Y, Brad Karpinka J, Karimi K, Zorn AM, Vize PD.
Genesis. 2015 Aug;53(8):486-97. doi: 10.1002/dvg.22873. Epub 2015 Jul 16.
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Last Updated: 2016-04-12